GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdB in Azospirillum brasilense Sp245

Align branched-chain-2-oxoacid decarboxylase (subunit 2/2) (EC 4.1.1.72) (characterized)
to candidate AZOBR_RS04800 AZOBR_RS04800 pyruvate dehydrogenase subunit beta

Query= BRENDA::Q9HIA4
         (319 letters)



>FitnessBrowser__azobra:AZOBR_RS04800
          Length = 343

 Score =  269 bits (687), Expect = 8e-77
 Identities = 154/332 (46%), Positives = 204/332 (61%), Gaps = 17/332 (5%)

Query: 1   MNMVQALNSAMDLKMSEDDSVIILGEDV-------GRD---GGVFRVTDGLQAKYGPQRV 50
           ++M  A+N A+DL+M  D +VI++GED+       G D   GGV  VT GL AK+G  R+
Sbjct: 5   ISMKTAINEALDLEMRRDPTVILMGEDIVGGTGAPGEDDAWGGVLGVTKGLFAKHG-DRL 63

Query: 51  IDTPLSELGIVGMAIGMAVNGLKPIPEIQFQDFIYTSMDQIINQMAKIRYRSGGDYTVPL 110
           +DTPLSE   +G AIG A  G++P+ E+ F DF+    DQI NQ AK RY  GG    P+
Sbjct: 64  LDTPLSESAYIGAAIGAATCGMRPVAELMFMDFMGVCFDQIFNQAAKFRYMFGGKAETPV 123

Query: 111 VLRTPVGGGIKGGLYHSQSGEAYFAHTAGLTVVSPSNPYDAKGLLISAIESPDPVIFLEP 170
           V+R  VG G +    HSQ     F H  GL VV PSN YDAKGLLI +I   DPVIF E 
Sbjct: 124 VIRGMVGAGFRAAAQHSQMLTPLFTHIPGLKVVCPSNAYDAKGLLIQSIRDNDPVIFCEH 183

Query: 171 KRLYRAQKVEVPDEKYTIPLRKANVLKQGNDVTIVTYGSMVPTVMSVA---SKSKYDVEV 227
           K LY   + EVP E Y IP  +ANVL+ G+ VTIV+YG  V   M  A   +K K + EV
Sbjct: 184 KNLY-GHETEVPAESYAIPFGEANVLRDGDHVTIVSYGLTVHRAMEAADALAKDKVEAEV 242

Query: 228 IDLRTIAPMDRDTIISSVKKTGRVVIVHEAPRTLGVGAEISAMISERAIEYLYAPIVRVT 287
           IDLRT++P+D DTII SV++TGR+V+V EA     +  +ISA +++ A   L + I  VT
Sbjct: 243 IDLRTLSPIDWDTIIDSVERTGRLVVVDEAHPRCNLATDISAFVAQNAFGALKSGIQMVT 302

Query: 288 GPDTPFPY--RLEEYYLPNEGRINAALDRVMS 317
            P TP P+   LE+ Y+P+   + AA+ R ++
Sbjct: 303 PPHTPVPFSPSLEDLYIPSAEAVAAAVRRTLA 334


Lambda     K      H
   0.318    0.137    0.388 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 304
Number of extensions: 13
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 319
Length of database: 343
Length adjustment: 28
Effective length of query: 291
Effective length of database: 315
Effective search space:    91665
Effective search space used:    91665
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory